Bush's big reorganization was to integrate FEMA (which is just a couple of thousand people) into a far larger bureaucracy, which has a very different mission than FEMA did. That is, if centralized command structures are prone to fail, then FEMA under Homeland Security under Bush is far more failure-prone than FEMA under Clinton was.

This is also not to say that FEMA was idyllic under Clinton. For instance in 1999, Hurricane Floyd overwhelmed it. However it did it's primary job - coordinating people and groups who want to help - than the current incarnation appears to be.

Cheers,
Ben